[package - main-amd64-default][science/rdkit] Failed for rdkit-2025.09.1 in build
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Date: Sat, 01 Nov 2025 06:15:30 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy24/data/main-amd64-default/p3613ba463b68_sc6e02892bb/logs/rdkit-2025.09.1.log
Build URL: https://pkg-status.freebsd.org/beefy24/build.html?mastername=main-amd64-default&build=p3613ba463b68_sc6e02892bb
Log:
=>> Building science/rdkit
build started at Sat Nov 1 06:13:25 -00 2025
port directory: /usr/ports/science/rdkit
package name: rdkit-2025.09.1
building for: FreeBSD main-amd64-default-job-12 16.0-CURRENT FreeBSD 16.0-CURRENT 1600003 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 4486 Nov 1 01:01 /usr/ports/science/rdkit/Makefile
Ports top last git commit: 3613ba463
Ports top unclean checkout: no
Port dir last git commit: 160a45c50
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.4
Host OSVERSION: 1600000
Jail OSVERSION: 1600003
Job Id: 12
!!! Jail is newer than host. (Jail: 1600003, Host: 1600000) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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===> The following configuration options are available for rdkit-2025.09.1:
DOCS=on: Build and/or install documentation
PGSQL=off: Build the PostgreSQL cartridge
PYTHON=on: Python bindings or support
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
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--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/science/rdkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/rdkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/rdkit/work/.cache HOME=/wrkdirs/usr/ports/science/rdkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/rdkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/rdkit/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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--End PLIST_SUB--
--SUB_LIST--
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#### ####
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# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
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=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> rdkit-2025.09.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.3.1_1.pkg
[main-amd64-default-job-12] Installing pkg-2.3.1_1...
[main-amd64-default-job-12] Extracting pkg-2.3.1_1: .......... done
===> rdkit-2025.09.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of rdkit-2025.09.1
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE accepted by the user
=> v1.3.3.tar.gz doesn't seem to exist in /portdistfiles/rdkit-2025.09.1.
=> Attempting to fetch https://github.com/schrodinger/maeparser/archive/v1.3.3.tar.gz
fetch: https://github.com/schrodinger/maeparser/archive/v1.3.3.tar.gz: size unknown
fetch: https://github.com/schrodinger/maeparser/archive/v1.3.3.tar.gz: size of remote file is not known
v1.3.3.tar.gz 38 kB 2178 kBps 00s
=> v3.0.2.tar.gz doesn't seem to exist in /portdistfiles/rdkit-2025.09.1.
=> Attempting to fetch https://github.com/schrodinger/coordgenlibs/archive/v3.0.2.tar.gz
fetch: https://github.com/schrodinger/coordgenlibs/archive/v3.0.2.tar.gz: size unknown
fetch: https://github.com/schrodinger/coordgenlibs/archive/v3.0.2.tar.gz: size of remote file is not known
v3.0.2.tar.gz 162 kB 3130 kBps 00s
=> v1.0.10 doesn't seem to exist in /portdistfiles/rdkit-2025.09.1.
=> Attempting to fetch https://codeload.github.com/Glysade/chemdraw/tar.gz/refs/tags/v1.0.10
fetch: https://codeload.github.com/Glysade/chemdraw/tar.gz/refs/tags/v1.0.10: size unknown
fetch: https://codeload.github.com/Glysade/chemdraw/tar.gz/refs/tags/v1.0.10: size of remote file is not known
v1.0.10 1019 kB 8399 kBps 01s
=> v1.1.0.tar.gz doesn't seem to exist in /portdistfiles/rdkit-2025.09.1.
=> Attempting to fetch https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz
fetch: https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz: size unknown
fetch: https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz: size of remote file is not known
v1.1.0.tar.gz 995 kB 8211 kBps 00s
=> ComicNeue-Regular.ttf doesn't seem to exist in /portdistfiles/rdkit-2025.09.1.
=> Attempting to fetch http://distcache.FreeBSD.org/local-distfiles/yuri/ComicNeue-Regular.ttf
ComicNeue-Regular.ttf 21 kB 94 MBps 00s
=> rdkit-rdkit-Release_2025_09_1_GH0.tar.gz doesn't seem to exist in /portdistfiles/rdkit-2025.09.1.
=> Attempting to fetch https://codeload.github.com/rdkit/rdkit/tar.gz/Release_2025_09_1?dummy=/rdkit-rdkit-Release_2025_09_1_GH0.tar.gz
fetch: https://codeload.github.com/rdkit/rdkit/tar.gz/Release_2025_09_1?dummy=/rdkit-rdkit-Release_2025_09_1_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/rdkit/rdkit/tar.gz/Release_2025_09_1?dummy=/rdkit-rdkit-Release_2025_09_1_GH0.tar.gz: size of remote file is not known
rdkit-rdkit-Release_2025_09_1_GH0.tar.gz 79 MB 13 MBps 06s
=> rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz doesn't seem to exist in /portdistfiles/rdkit-2025.09.1.
=> Attempting to fetch https://codeload.github.com/rareylab/RingDecomposerLib/tar.gz/v1.1.3_rdkit?dummy=/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz
fetch: https://codeload.github.com/rareylab/RingDecomposerLib/tar.gz/v1.1.3_rdkit?dummy=/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz: size unknown
<snip>
-- Looking for stdint.h - found
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for sys/stat.h
-- Looking for sys/stat.h - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Looking for getpagesize
-- Looking for getpagesize - found
-- Looking for bcopy
-- Looking for bcopy - found
-- Looking for memmove
-- Looking for memmove - found
-- Looking for mmap
-- Looking for mmap - found
-- HAVE_DLFXN_H=""
-- HAVE_FCNTL_H="1"
-- HAVE_INTTYPES_H="1"
-- HAVE_MEMORY_H="1"
-- HAVE_STDINT_H="1"
-- HAVE_STDLIB_H="1"
-- HAVE_STRINGS_H="1"
-- HAVE_STRING_H="1"
-- HAVE_SYS_STAT_H="1"
-- HAVE_SYS_TYPES_H="1"
-- HAVE_SYS_UNISTD_H=""
-- HAVE_GETPAGESIZE="1"
-- HAVE_BCOPY="1"
-- HAVE_MEMMOVE="1"
-- HAVE_MMAP="1"
-- Looking for 4 include files stdlib.h, ..., float.h
-- Looking for 4 include files stdlib.h, ..., float.h - found
-- Looking for off_t
-- Looking for off_t - not found
-- Looking for size_t
-- Looking for size_t - not found
== expat turn off warnings as errors when building
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Data/Fonts/ComicNeue-Regular.ttf already there, skipping the download
-- Found PkgConfig: /usr/local/bin/pkgconf (found version "2.4.3")
-- Found Cairo: /usr/local/include/cairo
-- Found Freetype: /usr/local/lib/libfreetype.so (found version "2.14.1")
Downloading file:///portdistfiles/rdkit-2025.09.1/v1.1.0.tar.gz...
-- Configuring done (8.5s)
-- Generating done (0.7s)
CMake Warning:
Manually-specified variables were not used by the project:
BOOST_PYTHON_SUFFIX
CATCH_DIR
CMAKE_COLOR_MAKEFILE
CMAKE_VERBOSE_MAKEFILE
Python_ADDITIONAL_VERSIONS
Python_EXECUTABLE
RDK_OPTIMIZE_NATIVE
-- Build files have been written to: /wrkdirs/usr/ports/science/rdkit/work/.build
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for rdkit-2025.09.1
[ 0% 3/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-alias
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[ 1% 11/804] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitRDGeneral.so.1.2025.09.1 lib/libRDKitRDGeneral.so.1 lib/libRDKitRDGeneral.so && :
[ 1% 12/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-alias
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[ 1% 15/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-alias
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[ 1% 16/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_OPTIMIZE_POPCNT -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-alias
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[ 5% 47/804] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitRDGeometryLib.so.1.2025.09.1 lib/libRDKitRDGeometryLib.so.1 lib/libRDKitRDGeometryLib.so && :
[ 5% 48/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -mpopcnt
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[ 6% 54/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -mpopcnt
-Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -DNDEBUG -std=gnu++20 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/ROMol.cpp
[ 6% 55/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -mpopcnt
-Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -DNDEBUG -std=gnu++20 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/PeriodicTable.cpp
[ 6% 56/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -mpopcnt
-Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -DNDEBUG -std=gnu++20 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/atomic_data.cpp
[ 6% 57/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -mpopcnt
-Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -DNDEBUG -std=gnu++20 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/RWMol.cpp
[ 6% 58/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -mpopcnt
-Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -DNDEBUG -std=gnu++20 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/QueryOps.cpp
[ 7% 59/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -mpopcnt
-Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -DNDEBUG -std=gnu++20 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/Canon.cpp
FAILED: [code=1] Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o
/usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -mpopcnt -Wall -Wextra
-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -DNDEBUG -std=gnu++20 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/Canon.cpp
Assertion failed: (VDecl->isLinkageValid()), function DeduceVariableDeclarationType, file /usr/local/poudriere/jails/main-amd64/usr/src/contrib/llvm-project/clang/lib/Sema/SemaDecl.cpp, line 12951.
PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script.
Stack dump:
0. Program arguments: /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -m
popcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -DNDEBUG -std=gnu++20 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/Canon.cpp
1. /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/Canon.cpp:87:2: current parser token ';'
2. /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/Canon.cpp:22:1: parsing namespace 'RDKit'
3. /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/Canon.cpp:23:1: parsing namespace 'RDKit::Canon'
#0 0x000027dc2559b4a9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x419b4a9)
#1 0x000027dc25599215 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x4199215)
#2 0x000027dc25542012 (/usr/lib/libprivatellvm.so.19+0x4142012)
#3 0x000027dc286b699c (/lib/libthr.so.3+0x1a99c)
#4 0x000027dc286b5fab (/lib/libthr.so.3+0x19fab)
#5 0x000027dc196e02d3 ([vdso]+0x2d3)
#6 0x000027dc2de06a9a __sys_thr_kill (/lib/libsys.so.7+0x19a9a)
#7 0x000027dc2be920d4 _raise (/lib/libc.so.7+0xc60d4)
#8 0x000027dc2bf43489 abort (/lib/libc.so.7+0x177489)
#9 0x000027dc2be74cc1 (/lib/libc.so.7+0xa8cc1)
#10 0x000027dc1e74cb12 clang::Sema::DeduceVariableDeclarationType(clang::VarDecl*, bool, clang::Expr*) (/usr/lib/libprivateclang.so.19+0x354cb12)
#11 0x000027dc1e74d1ae clang::Sema::AddInitializerToDecl(clang::Decl*, clang::Expr*, bool) (/usr/lib/libprivateclang.so.19+0x354d1ae)
#12 0x000027dc1e39a395 clang::Parser::ParseDeclarationAfterDeclaratorAndAttributes(clang::Declarator&, clang::Parser::ParsedTemplateInfo const&, clang::Parser::ForRangeInit*) (/usr/lib/libprivateclang.so.19+0x319a395)
#13 0x000027dc1e396ce4 clang::Parser::ParseDeclGroup(clang::ParsingDeclSpec&, clang::DeclaratorContext, clang::ParsedAttributes&, clang::Parser::ParsedTemplateInfo&, clang::SourceLocation*, clang::Parser::ForRangeInit*) (/usr/lib/libprivateclang.so.19+0x3196ce4)
#14 0x000027dc1e47a2a3 clang::Parser::ParseDeclOrFunctionDefInternal(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x327a2a3)
#15 0x000027dc1e479a89 clang::Parser::ParseDeclarationOrFunctionDefinition(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x3279a89)
#16 0x000027dc1e478850 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x3278850)
#17 0x000027dc1e3ba0ad clang::Parser::ParseInnerNamespace(llvm::SmallVector<clang::Parser::InnerNamespaceInfo, 4u> const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (/usr/lib/libprivateclang.so.19+0x31ba0ad)
#18 0x000027dc1e3b96df clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x31b96df)
#19 0x000027dc1e3956f6 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x31956f6)
#20 0x000027dc1e478433 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x3278433)
#21 0x000027dc1e3ba0ad clang::Parser::ParseInnerNamespace(llvm::SmallVector<clang::Parser::InnerNamespaceInfo, 4u> const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (/usr/lib/libprivateclang.so.19+0x31ba0ad)
#22 0x000027dc1e3b96df clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x31b96df)
#23 0x000027dc1e3956f6 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x31956f6)
#24 0x000027dc1e478433 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x3278433)
#25 0x000027dc1e476818 clang::Parser::ParseTopLevelDecl(clang::OpaquePtr<clang::DeclGroupRef>&, clang::Sema::ModuleImportState&) (/usr/lib/libprivateclang.so.19+0x3276818)
#26 0x000027dc1e3803ee clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x31803ee)
#27 0x000027dc1e1eebe2 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2feebe2)
#28 0x000027dc1e16122d clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2f6122d)
#29 0x000027dc1e282605 clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x3082605)
#30 0x000027d3f8397051 (/usr/bin/c+++0xf051)
#31 0x000027d3f83a52df (/usr/bin/c+++0x1d2df)
#32 0x000027dc1de088ae (/usr/lib/libprivateclang.so.19+0x2c088ae)
#33 0x000027dc25541d2c llvm::CrashRecoveryContext::RunSafely(llvm::function_ref<void ()>) (/usr/lib/libprivatellvm.so.19+0x4141d2c)
#34 0x000027dc1de07efa clang::driver::CC1Command::Execute(llvm::ArrayRef<std::__1::optional<llvm::StringRef>>, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>*, bool*) const (/usr/lib/libprivateclang.so.19+0x2c07efa)
#35 0x000027dc1ddc729e clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2bc729e)
#36 0x000027dc1ddc75ac clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl<std::__1::pair<int, clang::driver::Command const*>>&, bool) const (/usr/lib/libprivateclang.so.19+0x2bc75ac)
#37 0x000027dc1dde6390 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl<std::__1::pair<int, clang::driver::Command const*>>&) (/usr/lib/libprivateclang.so.19+0x2be6390)
#38 0x000027d3f83a48f8 (/usr/bin/c+++0x1c8f8)
#39 0x000027d3f83a2e72 (/usr/bin/c+++0x1ae72)
#40 0x000027dc2be66b0f __libc_start1 (/lib/libc.so.7+0x9ab0f)
c++: error: clang frontend command failed with exit code 134 (use -v to see invocation)
FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2)
Target: x86_64-unknown-freebsd16.0
Thread model: posix
InstalledDir: /usr/bin
Build config: +assertions
c++: note: diagnostic msg:
********************
PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
c++: note: diagnostic msg: /tmp/Canon-dd4b1e.cpp
c++: note: diagnostic msg: /tmp/Canon-dd4b1e.sh
c++: note: diagnostic msg:
********************
[ 7% 59/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -mpopcnt
-Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -DNDEBUG -std=gnu++20 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/AtomIterators.cpp
[ 7% 59/804] /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code -isystem /usr/local/include/eigen3 -isystem /usr/local/include -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -mpopcnt
-Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -D_GNU_SOURCE -fstack-protector-strong -fno-strict-aliasing -D_GNU_SOURCE -DNDEBUG -std=gnu++20 -fPIC -pthread -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -MF Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2025_09_1/Code/GraphMol/MolPickler.cpp
ninja: build stopped: subcommand failed.
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped making "build" in /usr/ports/science/rdkit